1 PhD project offered in the IPP winter call Molecular Mechanisms in Genome Stability & Gene Regulation

Scientific Background

Alternative splicing (AS) massively increases transcriptome complexity in higher eukaryotes, with critical implications in developmental processes and stress responses. Studying AS events in model systems revealed the existence of diverse regulatory principles, however, the mechanisms by which rapid and coordinated changes in the AS output can be achieved are still poorly understood. The Wachter group and others have previously shown that early seedling photomorphogenesis is accompanied and driven by AS changes. Furthermore, several splicing regulatory proteins involved in light-dependent AS and seedling development have been identified. In our ongoing research, we examine the molecular mechanisms and signaling pathways underlying rapid re-programming of the transcriptome via AS to steer seedling development in a light-dependent manner.

PhD Project: Regulation of alternative splicing by R-loop formation in Arabidopsis

R-loops refer to RNA-DNA hybrid structures that have been linked to genotoxic stress. More recently, R-loops have also been shown to function in the regulation of gene expression. A previous study generating a genome-wide R-loop atlas for the model plant Arabidopsis thaliana using ssDRIP-seq (single-strand DNA ligation-based library preparation from DNA:RNA hybrid immunoprecipitation followed by sequencing) identified major changes in R-loop formation in the comparison of dark- and light-grown seedlings (Xu et al., 2020). Furthermore, the Wachter group has demonstrated rapid re-programming of alternative splicing (AS) upon exposing etiolated seedlings to light (Hartmann et al., 2016; Saile et al., 2023). In this project, we would like to examine whether the occurrence of R-loops and AS are more widely coupled and will address in the context of the 4R RTG “R-loop Regulation in Robustness and Resilience” the following major questions: i) Are R-loops overrepresented in regions displaying light-dependent AS? ii) Does light exposure of dark-grown seedlings alter R-loop formation as quickly as changes occur on the level of AS? Here, it is planned to test the effects of photosynthetically active white light and genotoxic UV-B light. iii) Do mutants with altered expression of nuclear RNase H1, including gene knockouts and inducible expression lines, show alterations in their light responses, considering R-loop formation, AS, and development? Resolving these questions will also provide a basis to further study the mechanistic link between R-loops and AS in the future.

This project will be part of the RTG on R-loop Regulation in Robustness and Resilience (4R).

If you are interested in this project, please select Wachter as your group preference in the IPP application platform.

Publications relevant to this project

Conn VM, Hugouvieux V, Nayak A, Conos SA, Capovilla G, Cildir G, Jourdain A, Tergaonkar V, Schmid M, Zubieta C and Conn SJ (2017) A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation. Nat Plants, 3:17053 Link

Hartmann L, Drewe-Boß P, Wießner T, Wagner G, Geue S, Lee HC, Obermüller DM, Kahles A, Behr J, Sinz FH, Rätsch G, Wachter A (2016) Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis. Plant Cell, 28:2715-2734 Link

Saile J, Wießner-Kroh T, Erbstein K, Obermüller DM, Pfeiffer A, Janocha D, Lohmann J, Wachter A (2023). SNF1-RELATED KINASE 1 and TARGET OF RAPAMYCIN control light-responsive splicing events and developmental characteristics in etiolated Arabidopsis seedlings. Plant Cell 35: 3413-3428. Link

Xu W, Li K, Li S, Hou Q, Zhang Y, Liu K and Sun Q (2020) The R-loop atlas of Arabidopsis development and responses to environmental stimuli. Plant Cell, 32:888–903 Link